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Marcogliese PC, Deal SL, Andrews J, Harnish JM, Bhavana VH, Graves HK, Jangam S, Luo X, Liu N, Bei D, Chao YH, Hull B, Lee PT, Pan H, Bhadane P, Huang MC, Longley CM, Chao HT, Chung HL, Haelterman NA, Kanca O, Manivannan SN, Rossetti LZ, German RJ, Gerard A, Schwaibold EMC, Fehr S, Guerrini R, Vetro A, England E, Murali CN, Barakat TS, van Dooren MF, Wilke M, van Slegtenhorst M, Lesca G, Sabatier I, Chatron N, Brownstein CA, Madden JA, Agrawal PB, Keren B, Courtin T, Perrin L, Brugger M, Roser T, Leiz S, Mau-Them FT, Delanne J, Sukarova-Angelovska E, Trajkova S, Rosenhahn E, Strehlow V, Platzer K, Keller R, Pavinato L, Brusco A, Rosenfeld JA, Marom R, Wangler MF, Yamamoto S. Drosophila functional screening of de novo variants in autism uncovers damaging variants and facilitates discovery of rare neurodevelopmental diseases. Cell Rep 2022; 38:110517. [PMID: 35294868 PMCID: PMC8983390 DOI: 10.1016/j.celrep.2022.110517] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/23/2021] [Accepted: 02/18/2022] [Indexed: 12/30/2022] Open
Abstract
Individuals with autism spectrum disorder (ASD) exhibit an increased burden of de novo mutations (DNMs) in a broadening range of genes. While these studies have implicated hundreds of genes in ASD pathogenesis, which DNMs cause functional consequences in vivo remains unclear. We functionally test the effects of ASD missense DNMs using Drosophila through "humanization" rescue and overexpression-based strategies. We examine 79 ASD variants in 74 genes identified in the Simons Simplex Collection and find 38% of them to cause functional alterations. Moreover, we identify GLRA2 as the cause of a spectrum of neurodevelopmental phenotypes beyond ASD in 13 previously undiagnosed subjects. Functional characterization of variants in ASD candidate genes points to conserved neurobiological mechanisms and facilitates gene discovery for rare neurodevelopmental diseases.
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Affiliation(s)
- Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Samantha L Deal
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Jonathan Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - J Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - V Hemanjani Bhavana
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hillary K Graves
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sharayu Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Hematology/Oncology, BCM, Houston, TX 77030, USA
| | - Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Yu-Hsin Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Brooke Hull
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pradnya Bhadane
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Mei-Chu Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Colleen M Longley
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Nele A Haelterman
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sathiya N Manivannan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Linda Z Rossetti
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | | | - Sarah Fehr
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Annalisa Vetro
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Eleina England
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Isabelle Sabatier
- Department of Pediatric Neurology, Lyon University Hospitals, Lyon, France
| | - Nicolas Chatron
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Thomas Courtin
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Laurence Perrin
- Genetic Department, Robert Debré Hospital, APHP.Nord-Université de Paris, Paris 75019, France
| | - Melanie Brugger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Timo Roser
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Lindwurmstraße 4, 80337 Munich, Germany
| | - Steffen Leiz
- Department of Pediatrics and Adolescent Medicine, Hospital Dritter Orden, Munich, Germany
| | - Frederic Tran Mau-Them
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France; Laboratoire de Génétique, Innovation en Diagnostic Génomique des Maladies Rares UF6254, Plateau Technique de Biologie, CHU Dijon, 14 Rue Paul Gaffarel, BP 77908, 21079 Dijon, France
| | - Julian Delanne
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, Republic of Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Erik Rosenhahn
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Roberto Keller
- Adult Autism Center, Mental Health Department, Health Unit ASL Città di Torino, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy; Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, Turin, Italy
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
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Wang J, Rousseau J, Kim E, Ehresmann S, Cheng YT, Duraine L, Zuo Z, Park YJ, Li-Kroeger D, Bi W, Wong LJ, Rosenfeld J, Gleeson J, Faqeih E, Alkuraya FS, Wierenga KJ, Chen J, Afenjar A, Nava C, Doummar D, Keren B, Juusola J, Grompe M, Bellen HJ, Campeau PM. Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and Lysosomal Dysfunction. Am J Hum Genet 2019; 105:1237-1253. [PMID: 31785787 PMCID: PMC6904826 DOI: 10.1016/j.ajhg.2019.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/01/2019] [Indexed: 12/28/2022] Open
Abstract
We report an early-onset autosomal-recessive neurological disease with cerebellar atrophy and lysosomal dysfunction. We identified bi-allelic loss-of-function (LoF) variants in Oxidative Resistance 1 (OXR1) in five individuals from three families; these individuals presented with a history of severe global developmental delay, current intellectual disability, language delay, cerebellar atrophy, and seizures. While OXR1 is known to play a role in oxidative stress resistance, its molecular functions are not well established. OXR1 contains three conserved domains: LysM, GRAM, and TLDc. The gene encodes at least six transcripts, including some that only consist of the C-terminal TLDc domain. We utilized Drosophila to assess the phenotypes associated with loss of mustard (mtd), the fly homolog of OXR1. Strong LoF mutants exhibit late pupal lethality or pupal eclosion defects. Interestingly, although mtd encodes 26 transcripts, severe LoF and null mutations can be rescued by a single short human OXR1 cDNA that only contains the TLDc domain. Similar rescue is observed with the TLDc domain of NCOA7, another human homolog of mtd. Loss of mtd in neurons leads to massive cell loss, early death, and an accumulation of aberrant lysosomal structures, similar to what we observe in fibroblasts of affected individuals. Our data indicate that mtd and OXR1 are required for proper lysosomal function; this is consistent with observations that NCOA7 is required for lysosomal acidification.
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Affiliation(s)
- Julia Wang
- Program in Developmental Biology, Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justine Rousseau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada
| | - Emily Kim
- Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
| | - Sophie Ehresmann
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada
| | - Yi-Ting Cheng
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lita Duraine
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ye-Jin Park
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Gleeson
- Rady Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eissa Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, 11525, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11525, Saudi Arabia
| | - Klaas J Wierenga
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 26901, USA; Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Jiani Chen
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 26901, USA; Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra Afenjar
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France; Département de Génétique et Embryologie Médicale, CRMR des Malformations et Maladies Congénitales du Cervelet, GRC ConCer-LD, Sorbonne Universités, Hôpital Trousseau, Paris, 75012 France
| | - Caroline Nava
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France
| | - Diane Doummar
- Assistance Publique des Hôpitaux de Paris, Service de Neuropédiatrie, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012 France
| | - Boris Keren
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France
| | | | - Markus Grompe
- Department of Pediatrics, Oregon Health and Science University, Portland, Oregon 97201, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97201, USA
| | - Hugo J Bellen
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada.
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